The numbered subway lines — the system’s busiest — are slower than their lettered counterparts and routinely arrive at their terminals behind schedule, according to new MTA statistics.

The on-time performance rate — which monitors whether trains get to their last stop within five minutes of their scheduled time — for numbered lines was only 76.6 percent in September, the latest month for which statistics are available.

That means nearly a third of the trains were more than five minutes late to their final stop — well below the systemwide average of 83.6 percent.

One segment of the letter lines — the B, J/Z, L, M, N, Q, R and Franklin Avenue Shuttle, formerly known as the BMT — arrived on time at final terminals 89.9 percent of the time in September, according to the MTA.

Another segment — the A, C, D, E, F and G lines, formerly known as the IND — had an 87 percent on-time rate for that same month.

Numbered lines, formerly the IRT, suffer because they’re the busiest and often hit delays because of sick passengers and overcrowding, said Carmen Bianco, vice president of subways at New York City Transit.

“It doesn’t take much to back things up,” he said. “We could have 20 trains late for one sick person.”

He also said trains’ arriving late at their endpoints doesn’t necessarily translate to customers waiting longer, since riders aren’t typically following a schedule for service.

“What’s important is every five minutes the trains come and they go and they’re on their way,” he said.

Still, August was no better for the numbered lines; trains were late 24.4 percent of the time. The systemwide average for late trains was 17.9 percent.

The lettered lines’ on-time performance rates were also higher in August.

The “BMT” letter lines were late only 10 percent of the time in August, and the “IND” lines were late 17.2 percent of the time.

Much of the numbered lines’ delayed performance can be attributed to the 2 train. That line was on schedule only 57 percent of the time in September and 53.5 percent in August — the worst performance rate of any of the lines in the system for both of those months.

The 4 line is also frequently late. The East Side subway line — one of the busiest subways in North America — was on time only 63.7 percent of the time.

The main subway line with the best on-time performance rate was the L — with a near-perfect 96.1 percent rating.